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Sample GSM2977444 Query DataSets for GSM2977444
Status Public on Feb 01, 2019
Title Uninfected rice plants, bio rep 2
Sample type RNA
 
Source name 25 days old rice seedlings
Organism Oryza sativa
Characteristics genotype: Rice line carrying bacterial blight and blast resistance gene Xa21, xa13 and Pi54 respectively
age: 25 days old rice seedlings
infection: uninfected
Treatment protocol For bacterial blight infection, the rice leaves were clip inoculated with Xanthomonas oryzae pv. oryzae isolate (DX-020), by dipping the scissors in saturated culture of Xoo and cutting the leaf tips so that the cells are deposited at the site of incision. For blast infection, the fungal spore suspension of Magnaporthe oryzae isolate (SP-28) was sprayed in conditions of hight humidity to facilitate heavy infection.
Growth protocol Rice plants were grown in platic trays under green house conditions.
Extracted molecule total RNA
Extraction protocol 2 cm rice tissue was collected from the leaves below the point of Xoo inocluation and where the fungal spores were sprayed, 10-15 such leaf pieces for each biological replicate were collected and processed for RNA isolation using TRIZOL (Invitrogen). The tissue was collected and RNA was extracted at two time points 24 and 72 hrs post infection, RNA was then pooled from these two time points.
Label Biotin
Label protocol 250ng of total RNA from pooled sample was converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
 
Hybridization protocol The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
Scan protocol The gene chips were scanned on an Affymetrix Scanner 3000
Description Expression profile of uninfected rice plants, 24 and 72 hrs post infection.
Data processing The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 13.1 - GX - PA (Agilent Technology) for further analysis. The PLIER 16 algorithm was used for data normalization
 
Submission date Feb 02, 2018
Last update date Feb 01, 2019
Contact name Ramesh V. Sonti
E-mail(s) sonti@ccmb.res.in
Organization name Centre for cellular and molecular biology (CCMB)
Department Plant Microbe Interactions
Street address Uppal Road
City Hyderabad
State/province Andhra Pradesh
ZIP/Postal code 500007
Country India
 
Platform ID GPL2025
Series (1)
GSE110088 Transcriptional profiling of rice gene expression changes upon co-infection with pathogens Magnapothe oryzae and Xanthomonas oryzae pv. oryzae that causes rice blast and bacterial blight respectively.

Data table header descriptions
ID_REF
VALUE PLIER 16

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.170942
AFFX-BioB-M_at 8.519404
AFFX-BioB-3_at 8.202224
AFFX-BioC-5_at 9.138357
AFFX-BioC-3_at 9.510249
AFFX-BioDn-5_at 10.940048
AFFX-BioDn-3_at 11.318751
AFFX-CreX-5_at 12.62413
AFFX-CreX-3_at 12.705415
AFFX-DapX-5_at 7.6145897
AFFX-DapX-M_at 9.775
AFFX-DapX-3_at 10.5889
AFFX-LysX-5_at 6.2265053
AFFX-LysX-M_at 6.831541
AFFX-LysX-3_at 8.023416
AFFX-PheX-5_at 6.8983006
AFFX-PheX-M_at 7.2591877
AFFX-PheX-3_at 7.6081486
AFFX-ThrX-5_at 5.7857556
AFFX-ThrX-M_at 7.5430083

Total number of rows: 57381

Table truncated, full table size 1590 Kbytes.




Supplementary file Size Download File type/resource
GSM2977444_BBCtrl-2_Rice_.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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